Methods for Treating Breast Cancer and for Identifying Breast Cancer Antigens

ABSTRACT

Disclosed herein are isolated compositions including at least 2 of mutant peptides selected from the group consisting of SEQ ID NOS: 1-149, or polypeptides comprising the mutant peptides; wherein the composition comprises mutant peptides encoded by 2 or more genes. Also disclosed are methods for personalized treatment of breast cancer involving creating a peptide array of mutant peptides comprising the mutations in protein-encoding regions of the high-frequency cancer genes or the exome in a subject and screening the peptide array with a biological sample from the subject to detect antibodies in the biological sample that bind to the array, to detect antigenic targets for therapy in treating the subject.

CROSS REFERENCE

This application is a Divisional application of U.S. patent application Ser. No. 15/990,172, filed on May 25, 2018, which claims priority to U.S. Provisional Patent Application Ser. No. 62/511,767 filed May 26, 2017, incorporated by reference herein in its entirety.

BACKGROUND

Recent advances in cancer immuno-therapeutics such as checkpoint inhibitors, chimeric antigen-receptor T cells, and tumor infiltrating T cells (TIL) are now significantly impacting cancer patients in a positive manner. Although very promising, reports indicate no more than 25% of cases result in complete remission. One of the limitations of these treatments is the identity of putative cancer antigens in each patient as it is technically challenging to identify of cancer antigens in a rapid fashion. Thus, identification of cancer antigens followed by targeted treatment will increase the efficacy of cancer immunotherapies.

SUMMARY

In one aspect the disclosure provides isolated compositions comprising at least 2 of the mutant peptides selected from the group consisting of SEQ ID NOS: 1-149, or polypeptides comprising the mutant peptides; wherein the composition comprises mutant peptides encoded by 2 or more genes. In one embodiment, the composition further comprises one or more wild type peptides corresponding to the mutant peptides, or polypeptides comprising the wild type peptides. In another embodiment, the total number of mutant and wild type peptides, or polypeptides comprising the mutant and wild type peptides, is 100,000 or less. In further embodiments, the peptides may be detectably labeled, and/or the peptides may be immobilized on the surface of a solid support.

In another aspect the disclosure provides methods for personalized treatment of breast cancer, comprising:

(a) performing sequence analysis of high-frequency cancer genes, or performing whole exome sequencing on DNA from a biological sample from a subject having breast cancer;

(b) identifying mutations in protein-encoding regions of the high-frequency cancer genes or the exome;

(c) creating a peptide array of mutant peptides comprising the mutations in protein-encoding regions of the high-frequency cancer genes or the exome, and optionally comprising wild-type counterparts of the mutant peptides;

(d) contacting the peptide array with a biological sample from the subject for a time and under conditions to permit binding of antibodies in the serum to the mutant peptides and/or the wild-type counterparts thereof; and

(e) detecting binding of antibodies in the serum to the mutant peptides and/or the wild-type counterparts thereof, thus identifying antigenic targets for therapy in treating the subject.

In another aspect, the disclosure provides methods for monitoring breast cancer immunotherapy, comprising

(a) contacting a biological sample from a subject who is undergoing or has undergone breast cancer therapy with a peptide array prepared according to the methods of the disclosure, or with a composition of the invention; and

(b) determining an amount of antibodies against the one or more peptides in the bodily fluid sample;

wherein an increase in the amount of antibodies relative to a control, such as a baseline level of antibodies in a similar bodily fluid sample from the subject indicates efficacy of the breast cancer immunotherapy in the subject; or

wherein a decrease or no increase in the amount of antibodies relative to a control, such as a baseline level of antibodies in a similar bodily fluid sample from the subject indicates that the immunotherapy is ineffective in the subject.

DETAILED DESCRIPTION

All references cited are herein incorporated by reference in their entirety. Within this application, unless otherwise stated, the techniques utilized may be found in any of several well-known references such as: Molecular Cloning: A Laboratory Manual (Sambrook, et al., 1989, Cold Spring Harbor Laboratory Press), Gene Expression Technology (Methods in Enzymology, Vol. 185, edited by D. Goeddel, 1991. Academic Press, San Diego, Calif.), “Guide to Protein Purification” in Methods in Enzymology (M. P. Deutshcer, ed., (1990) Academic Press, Inc.); PCR Protocols: A Guide to Methods and Applications (Innis, et al. 1990. Academic Press, San Diego, Calif.), Culture of Animal Cells: A Manual of Basic Technique, 2^(nd) Ed. (R. I. Freshney. 1987. Liss, Inc. New York, N.Y.), and Gene Transfer and Expression Protocols, pp. 109-128, ed. E. J. Murray, The Humana Press Inc., Clifton, N.J.

As used herein, the singular forms “a”, “an” and “the” include plural referents unless the context clearly dictates otherwise. “And” as used herein is interchangeably used with “or” unless expressly stated otherwise.

All embodiments of any aspect of the disclosure can be used in combination, unless the context clearly dictates otherwise.

Disclosed herein in a first aspect are isolated compositions, comprising at least 2 of the peptides selected from the group consisting of SEQ ID NOS: 1-149, or polypeptides comprising the peptides; wherein the composition comprises peptides encoded by 2 or more genes. As described in the examples below, peptides comprising or consisting of the amino acid sequence of SEQ ID NOS:1-149 were identified as tumor antigens from human breast cancer (BCa) patients, with the antigens being mutant peptides arising from single nucleotide variants (SNVs), as well as insertions and deletions that results into frame-shift mutations. Thus, the compositions may be used, for example, in identifying patient-specific tumor antigens for patient-specific immunotherapeutics. In one embodiment, the compositions may be contacted with antibodies from a patient (such as a patient having BCa) to identify the tumor antigens that are generating an immune response (positive antigens) in the patient. Antibodies against such positive antigens may then be generated/administered to the patient as an immunotherapeutic.

In various embodiments, the composition comprises least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, or all 149 of the peptides having the amino acid sequence of SEQ ID NO:149, or polypeptides comprising peptides having the amino acid sequence of SEQ ID NOS: 1-149.

In other embodiments, the composition comprises mutant peptides encoded by 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, or all 90 genes listed in Table 1.

TABLE 1 (149 mutants; 90 genes)) Highest Sample Gene Mutation Mutant peptide mut/wt Type AADACL3 L350P SMRILSALVQFVKGP (SEQ ID NO: 1) 2.1 malignant ABCF1 del4-218_218 SVLRSSQCQPVMRRM (SEQ ID NO: 2) 2.9 malignant ABCF1 del7-218_218 PAEGRKPRVVMFLQP (SEQ ID NO: 3) 2.1 malignant ADAM12 G479E DCQLKPAETACRDSS (SEQ ID NO: 4) 2.7 malignant AKAP6 P1839T SSSEMTNTSDTLNIE (SEQ ID NO: 5) 2.3 malignant ALPK2 P1449S GHEAEIQSAILQVPC (SEQ ID NO: 6) 2.2 malignant APC del3-4260_4260 AEVKHLHHLLKQLKP (SEQ ID NO: 7) 2 malignant APC del6-4731_4734 TGCNPKSMLVLHRGM (SEQ ID NO: 8) 2.8 malignant APC del1-3920_3924 DSANTLQIAERKDWN (SEQ ID NO: 9) 2.2 malignant ATR D564H LDLEATIHKVVKIYD (SEQ ID NO: 10) 2.2 malignant BAIAP2L2 del1-1322_1363 LDRPGNSTPSRVPSR (SEQ ID NO: 11) 2 malignant BAX del1-114_114 RAGRMGGRHPSWPWT (SEQ ID 2.3 malignant NO: 12) BGN K288N ELHLDNNNLARVPSG (SEQ ID NO: 13) 2.6 benign BRAF V600E GDFGLATEKSRWSGS (SEQ ID NO: 14) 1.8 benign BRCA1 E1038G IRENVFKGASSSNIN (SEQ ID NO: 15) 2 malignant BRD3 del2-71_71 PTPASPAARPTSCST (SEQ ID NO: 16) 2 malignant BRSK1 ins3-1127_1127 EAATRAEVHGSPEHH (SEQ ID NO: 17) 2 malignant C04A2 G67D RGQPGPVDPQGYNGP (SEQ ID NO: 18) 2 malignant CALR del2-1095_1140 RRMMRTKMRMRRMRR (SEQ ID 2.7 malignant NO: 19) CALR del4-1095_1140 RRKMSPARPRTSCRA (SEQ ID NO: 20) 2.3 malignant CALR del2-1092_1143 MMRTKMRMRRMRRTR (SEQ ID 2.3 malignant NO: 21) CALR del3-1102_1135 MRMRRMRRTRRKMRR (SEQ ID 2.8 malignant NO: 22) CDC42EP1 del1-758_778 NPPAPAATPTGPAAN (SEQ ID NO: 23) 2.3 malignant CDKN2A del1-233_234 NCADPATHPTRARRC (SEQ ID NO: 24) 4.1 malignant CDKN2A del187 SARVAELTAPTPPLS (SEQ ID NO: 25) 10.5 malignant CDKN2A del2-233_234 RARRCPGGLPGHAGG (SEQ ID NO: 26) 2.3 malignant CDKN2A del3-233_234 GHAGGAAPGRGAAGR (SEQ ID 2.7 malignant NO: 27) CEBPA del5-26_26 ASTRRPSTSAPTSTR (SEQ ID NO: 28) 3.9 malignant CEBPA del6-26_26 PTSTRPPSTTSSWPT (SEQ ID NO: 29) 2.2 malignant CEBPA ins5-27_27 RARDVHRHQRLHRPG (SEQ ID NO: 30) 2.4 malignant CEBPA ins6-27_27 LHRPGRLQRRVPGRP (SEQ ID NO: 31) 2 malignant CEBPA ins8-27_27 AAGEGQGGRGPHGRR (SEQ ID 2.3 malignant NO: 32) CEP164 del3-337_337 RTETPPKVRWPWVPH (SEQ ID NO: 33) 3 malignant CHEK2 K373E ITDFGHSEILGETSL (SEQ ID NO: 34) 2.7 malignant CLASRP L198S VEVDVDESNQEQVAD (SEQ ID NO: 35) 8.5 malignant COBLL1 del1-2720_2720 AKPSSFFCRCRREYR (SEQ ID NO: 36) 2.2 malignant CRIPAK del12-295_323 TCRCGVPACSHVPMR (SEQ ID NO: 37) 2.2 malignant CRIPAK del10-205_206 HAECPPAHTCRRGVP (SEQ ID NO: 38) 2.9 malignant CTCF ins3-610_610 LYRGGQRCRCVCLRF (SEQ ID NO: 39) 2.4 malignant CTNNB1 A43V HSGATTTVPSLSGKG (SEQ ID NO: 40) 3.9 malignant CTNNB1 del1-14_241 MATQDIDGQYAMTRA (SEQ ID 2.2 malignant NO: 41) DLEC1 del1-5312_5314 HNGLSLGPHMSSELT (SEQ ID NO: 42) 2.5 malignant DPP6 D475N SQPNSSNNNIQSITS (SEQ ID NO: 43) 2.2 benign DTX3L K209N SPSMTERNPLSQQER (SEQ ID NO: 44) 9 malignant DUOX1 R76G EPHLPNPGDLSNTIS (SEQ ID NO: 45) 2.5 malignant EGFR del1-2237_2254 KIPVAIKAPKANKEI (SEQ ID NO: 46) 4.1 malignant EGFR del1-2238_2252 IPVAIKESPKANKEI (SEQ ID NO: 47) 5.2 malignant EGFR del1-2238_2255 KIPVAIKDPKANKEI (SEQ ID NO: 48) 4.9 malignant EGFR del1-2239_2256 IPVAIKEPKANKEIL (SEQ ID NO: 49) 2.6 malignant EGFR del1-2240_2257 IPVAIKESKANKEIL (SEQ ID NO: 50) 2.5 malignant EGFR E709K ALLRILKKTEFKKIK (SEQ ID NO: 51) 2 malignant EVX1 R407T SSVALDQREEVPLTT (SEQ ID NO: 52) 2 malignant FAM157A del1-210_218 QQQQQQQLDLLFHQR (SEQ ID NO: 53) 2 malignant GPRASP2 D324V KLRTNREVCFESESE (SEQ ID NO: 54) 2.9 malignant GPS2 Q240E HGHFQPTETGFLQPG (SEQ ID NO: 55) 3.6 malignant HDGFRP2 del1-1721_1722 EKEKAEETGRGGAGR (SEQ ID NO: 56) 2.2 malignant HDGFRP2 del2-1721_1722 GGAGRGGGPPGEGGG (SEQ ID NO: 57) 3.2 malignant HDGFRP2 del5-1721_1722 ITEGGERRGQGARGG (SEQ ID NO: 58) 3.4 malignant HDGFRP2 del6-1721_1722 GARGGSGLGGGAKVW (SEQ ID 2.1 malignant NO: 59) HDGFRP2 del7-1721_1722 RGGSGLGGGAKVWLL (SEQ ID 2.1 malignant NO: 60) HEG1 A193E VGYSLEIETALTSQS (SEQ ID NO: 61) 2.8 malignant HLA-B ins3-207_207 VLGPEHTDLQGPGTD (SEQ ID NO: 62) 2.4 malignant HLA-DRB1 del1-301_301 KDILEQAGPRWTPTA (SEQ ID NO: 63) 3.4 malignant HLA-DRB1 ins1-298_298| QKDILEQERGPRWTP (SEQ ID NO: 64) 5.3 malignant HOXB1 ins1-83_83 AYSAHSAHSAPTSFP (SEQ ID NO: 65) 2.9 malignant IPYR K57N VPRWSNANMEIATKD (SEQ ID NO: 66) 10.1 malignant JPH4 del1-1504_1504 AWPEEWGGQAHRQRN (SEQ ID 2.1 malignant NO: 67) JPH4 ins1-1505_1505 PEEWGGARRTGRGTS (SEQ ID NO: 68) 2.1 malignant KIF6 A386E TGEQRTEELTEAELL (SEQ ID NO: 69) 2.2 malignant KRAS A59T LLDILDTTGQEEYSA (SEQ ID NO: 70) 1.8 malignant KRT76 L168V NQSLLQPVNVEIDPQ (SEQ ID NO: 71) 2.4 malignant LCN15 K164E YPTLGLPEDMMVMLP (SEQ ID NO: 72) 3.2 malignant MACF1 S3042T MGVLGPLTIDPNMLN (SEQ ID NO: 73) 2.2 malignant MAGEA4 G153D RCFPVIFDKASESLK (SEQ ID NO: 74) 12.9 malignant MAP3K1 del6-2824_2825 PFFFYPICTSWHCNR (SEQ ID NO: 75) 2.2 malignant MEN1 del2-249_252 SMPASPPRSEAPSTC (SEQ ID NO: 76) 2.4 malignant MEN1 ins1-1562_1562 AVSGPPREASWDCRW (SEQ ID NO: 77) 2.1 malignant MUC17 S1083P YSQASSSPTTADGTS (SEQ ID NO: 78) 4.3 malignant MUC17 T1608A KTQVTASAEASSSTT (SEQ ID NO: 79) 1.5 benign MUC17 T1784A STPVTTSAEATSSPT (SEQ ID NO: 80) 2.2 malignant MUC17 T2786A SIPVTTSAEASSSPT (SEQ ID NO: 81) 4.6 malignant MUC17 T664A NTPVTTSAEATSSST (SEQ ID NO: 82) 2.3 malignant MUC17 T723A STPVTTSAEASSSPT (SEQ ID NO: 83) 4.5 malignant MUC17 T959A STPVTTSAEATSSPT (SEQ ID NO: 84) 5.3 malignant MUC17 T664A NTPVTTSAEATSSST (SEQ ID NO: 85) 3.9 malignant MUC17 T959A STPVTTSAEATSSPT (SEQ ID NO: 86) 3.9 malignant MUC22 ins1-1044_1044 MAGSETTTVSTAGSE (SEQ ID NO: 87) 4.2 malignant MUC3A del3-1244_1245 GDFHNHDPIFSEYRH (SEQ ID NO: 88) 2.5 malignant MUC3A del6-1244_1245 YRFPDYSNRPHINIH (SEQ ID NO: 89) 2 malignant MUC6 ins8-4708_4708 HPYPCTDGHFCLHPL (SEQ ID NO: 90) 2.2 malignant MUC6 ins9-4708_4708 CLHPLNANRHDSSTD (SEQ ID NO: 91) 3.5 malignant MYOM1 R212K SKQSTASKQSTASRQ (SEQ ID NO: 92) 2.2 benign NCOR1 K178N ASPSKLSNEELIQSM (SEQ ID NO: 93) 2.5 malignant NCOR2 ins1-1529_1529 QQQQQQPDMPRSSQE (SEQ ID NO: 94) 3.5 malignant NCOR2 ins1-1529_1529 QQQQQQPDDDDMPRS (SEQ ID 2.2 malignant NO: 95) NEK3 E477K LEPGLDEKDTDFEEE (SEQ ID NO: 96) 2.6 malignant NFE2L2 E79K AQLQLDEKTGEFLPI (SEQ ID NO: 97) 2.3 malignant NKX28 V89G EKRKKRRGLFSKAQT (SEQ ID NO: 98) 2.1 malignant NPM1 ins1-777_777 DQEAIQDLWSAVEEV (SEQ ID NO: 99) 2.8 malignant NR2E3 D196N EDADENINVTSNDPE (SEQ ID NO: 100) 4.5 malignant NUP210 G1413E VHFHDNSEDVFHAHS (SEQ ID 2.8 malignant NO: 101) OR52D1 ins2-608_608 GSAGHGTGFHSHCHF (SEQ ID 3 malignant NO: 102) PCDH15 P69S IKGTAGGASDPTIELS (SEQ ID NO: 103) 3 malignant PCSK5 T1343M EKTCKECMPEFFLHD (SEQ ID 3 malignant NO: 104) PDE1B R394P ALMEEFFPQGDKEAE (SEQ ID 3.3 malignant NO: 105) PIK3R1 D560G AAEYREIGKRMNSIK (SEQ ID NO: 106) 2 malignant PIK3R1 G376R TLTLRKGRNNKLIKI (SEQ ID NO: 107) 2.2 malignant PLCB1 A907P SVLTEVEPQTIEELK (SEQ ID NO: 108) 2 malignant PRRC2A R1152H PPSPAPAHFTARGGR (SEQ ID NO: 109) 2.5 malignant PSMD1 K310N TSSAFVGNTPEASPE (SEQ ID NO: 110) 2 malignant RET G593E LRGSIVGEHEPGEPR (SEQ ID NO: 111) 1.7 malignant SCARF2 ins1-2304_2304 GPPRSAPRGCLHVGR (SEQ ID NO: 112) 2.2 malignant SF3B1 K666E QARHTGIEIVQQIAI (SEQ ID NO: 113) 1.5 benign SHROOM4 ins1-3384_3384 KQQQQQQQQQQKQQE (SEQ ID 2.8 malignant NO: 114) SLC3A2 del4-892_892 RTRGSPLRLTLWPPR (SEQ ID NO: 115) 2.2 malignant SLITRK1 R266Q DLCPLKNQVDSSLPA (SEQ ID NO: 116) 5 malignant SMAD4 D493H AAAGIGVHDLRRLCI (SEQ ID NO: 117) 3.4 malignant STX5 Q25H QTRQNGIHTNKPALR (SEQ ID 2.5 malignant NO: 118) SVIL del4-4308_4308 CVERCPWKGICWKWP (SEQ ID 2 malignant NO: 119) SYDE2 K937N ENDPGDSNYTVDLLD (SEQ ID 2.5 malignant NO: 121) TAB2 I466T NTKYTFKTTVSPNKP (SEQ ID NO: 121) 2 malignant TCERG1 del1-2800_2800 IEALTKKRESTLGNF (SEQ ID NO: 122) 2.3 malignant TP53 del1-466_466 STPPPGTASAPWPST (SEQ ID NO: 123) 2 malignant TP53 del2-439_439 HPRPAPASAPWPSTS (SEQ ID NO: 124) 2.5 malignant TP53 del2-526_526 MSAAQIAMVWPLLSI (SEQ ID 3.4 malignant NO: 125) TP53 del2-880_880 TSCPQGALSEHCPTT (SEQ ID NO: 126) 3.6 malignant TP53 del7-754_754 SEHCPTTPAPLPSQR (SEQ ID NO: 127) 2.2 malignant TP53 I255F RRPILTIFTLEDSSG (SEQ ID NO: 128) 2.3 benign TP53 I255N RRPILTINTLEDSSG (SEQ ID NO: 129) 2.8 malignant TP53 K132E TYSPALNEMFCQLAK (SEQ ID 1.6 malignant NO: 130) TP53 L252P GMNRRPIPTIITLED (SEQ ID NO: 131) 2.5 malignant TP53 R196P APPQHLIPVEGNLRV (SEQ ID NO: 132) 1.5 malignant TP53 R249M CMGGMNRMPILTIIT (SEQ ID NO: 133) 2.1 malignant TP53 R283P ACPGRDRPTEEENLR (SEQ ID NO: 134) 1.6 malignant TP53 R342P RERFEMFPELNEALE (SEQ ID NO: 135) 3 malignant TP53 Y220N RHSVVVPNEPPEVGS (SEQ ID NO: 136) 2.2 benign TP53 del1-598_598 HLIRVEGICVWSIWM (SEQ ID NO: 137) 2.1 malignant TP53 del1-751_751 GGMNRRPSSPSSHWK (SEQ ID 2.1 malignant NO: 138) TP53 del4-880_880 SQRRNHWMENISPFR (SEQ ID 2.1 malignant NO: 139) TP53 del5-835_835 APLPSQRRNHWMENI (SEQ ID 2 malignant NO: 140) TPO del2421 ADGAHPPATPLRGAE (SEQ ID 3 malignant NO: 141) WDR72 A788D KPSRKVDDSLTIDTA (SEQ ID NO: 142) 2 malignant ZC3H18 ins2-2101_2101 PPQEADAKRQRQWQW (SEQ ID 2.2 malignant NO: 143) ZC3H18 del1-2102_2102 RRKERPARTPPGGGR (SEQ ID NO: 144) 2 malignant ZDHHC8 del12- SACCAPRPTHSSATQ (SEQ ID NO: 145) 4.4 malignant 1369_1369 ZDHHC8 del18- ATLPCRRHCPRCPAP (SEQ ID NO: 146) 2.1 malignant 1369 1369 ZDHHC8 del2-1369_1369 VAFLPPMHCPTATAA (SEQ ID 2.1 malignant NO: 147) ZNF184 K206E SPEETSTERSIKQNS (SEQ ID NO: 148) 2 malignant ZNF605 S82C FGKIFNSCINIVHVG (SEQ ID NO: 149) 8.3 malignant

In any of these embodiments, the isolated composition may further comprise one or more wild type peptides corresponding to the mutant peptides, or polypeptides comprising the wild type peptides. These wild type peptides may, for example, serve as controls to help identify antibodies that specifically recognize the mutant peptide. In various embodiments, the composition may further comprise 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, or 149 wild type peptide counterparts to the mutant peptides of SEQ ID NOS:1-149, or polypeptides comprising the wild type peptides.

The composition may have any number of total peptides as deemed appropriate for a given use. In one embodiment, the total number of mutant and wild type peptides, or polypeptides comprising the mutant and wild type peptides, is 100,000 or less. In various further embodiments, the total number of mutant and wild type peptides, or polypeptides comprising the mutant and wild type peptides, is 75,000, 50,000, 25,000, 10,000, 7500, 5000, 2500, 1500, 1000, 950, 900, 850, 800, 750, 700, 650, 600, 550, 500, or less.

In all of the above embodiments, the peptides may be labeled with a detectable label. Any suitable detectable label can be used, including but not limited fluorescent labels. In one embodiment, the detectable labels for each peptide are distinguishable. Methods for detecting the label include, but are not limited to spectroscopic, photochemical, biochemical, immunochemical, physical or chemical techniques.

The compositions can be stored frozen, in lyophilized form, or as a solution. In one embodiment, the peptides may be immobilized on a surface of a solid support. Any suitable solid support may be used. Examples of such supports include, but are not limited to, microarrays, beads, columns, optical fibers, wipes, nitrocellulose, nylon, glass, quartz, diazotized membranes (paper or nylon), silicones, polyformaldehyde, cellulose, cellulose acetate, paper, ceramics, metals, metalloids, semiconductive materials, coated beads, magnetic particles; plastics such as polyethylene, polypropylene, and polystyrene; and gel-forming materials, such as proteins (e.g., gelatins), lipopolysaccharides, silicates, agarose, polyacrylamides, methylmethracrylate polymers; sol gels; porous polymer hydrogels; nanostructured surfaces; nanotubes (such as carbon nanotubes), and nanoparticles (such as gold nanoparticles or quantum dots). This embodiment facilitates use of the compositions in various detection assays.

In another aspect the disclosure provides methods for personalized treatment of breast cancer, comprising:

(a) performing sequence analysis of high-frequency cancer genes, or performing whole exome sequencing on DNA from a biological sample from a subject having breast cancer;

(b) identifying mutations in protein-encoding regions of the high-frequency cancer genes or the exome;

(c) creating a peptide array of mutant peptides comprising the mutations in protein-encoding regions of the high-frequency cancer genes or the exome, and optionally comprising wild-type counterparts of the mutant peptides;

(d) contacting the peptide array with a biological sample from the subject, for a time and under conditions to permit binding of antibodies in the serum (if present) to the mutant peptides and/or the wild-type counterparts thereof; and

(e) detecting binding of antibodies in the serum to the mutant peptides and/or the wild-type counterparts thereof, thus identifying antigenic targets for therapy in treating the subject.

As disclosed in the examples that follow, the inventor has used the methods disclosed herein to identify 149 tumor antigens from human breast cancer patients, used to develop the compositions disclosed herein. While not being bound by any specific mechanism of action, the inventor proposes a general model of anti-cancer immunity wherein the disclosed methods help identify patient-specific tumor antigens in a timely fashion for precision immunotherapies. Such methods can thus be used to generate patient-specific peptide arrays which can then be screened using antibodies in a biological sample from the patient, including but not limited to serum, to identify antigenic targets that can be further targeted for treatment in the patient by, for example, administering antibodies against the identified targets to treat breast cancer.

Performing sequence analysis of high-frequency cancer genes, or performing whole exome sequencing on DNA, can be carried out using any suitable technique, including but not limited to those disclosed in the examples.

Similarly, identifying mutations in protein-encoding regions of the high-frequency cancer genes or the exome can be carried out using any suitable technique and comparison to any suitable reference genes, including but not limited to those disclosed in the examples.

The peptide arrays generated as described above can be used in additional methods. In one embodiment, the peptide arrays can be used to monitor breast cancer immunotherapy, the method comprising:

(a) contacting a biological sample from a subject who is undergoing or has undergone breast cancer therapy with the peptide array; and

(b) determining an amount of antibodies against the one or more peptides in the bodily fluid sample;

wherein an increase in the amount of antibodies relative to a control, such as a baseline level of antibodies in a similar bodily fluid sample from the subject indicates efficacy of the breast cancer immunotherapy in the subject.

In one embodiment, the peptide arrays can be used to monitor breast cancer immunotherapy, the method comprising:

(a) contacting a biological sample from a subject who is undergoing or has undergone breast cancer therapy with the peptide array; and

(b) determining an amount of antibodies against the one or more peptides in the bodily fluid sample;

wherein a decrease or no increase in the amount of antibodies relative to a control, such as a baseline level of antibodies in a similar bodily fluid sample from the subject indicates that the immunotherapy is ineffective in the subject.

Disclosed herein in a further embodiment, are methods to monitor breast cancer immunotherapy, comprising:

(a) contacting a biological sample from a subject who is undergoing or has undergone breast cancer therapy with the composition of any embodiment or combination of embodiments of the disclosure; and

(b) determining an amount of antibodies against the one or more peptides in the bodily fluid sample;

wherein an increase in the amount of antibodies relative to a control, such as a baseline level of antibodies in a similar bodily fluid sample from the subject indicates efficacy of the breast cancer immunotherapy in the subject.

Disclosed herein in another embodiment, are methods to monitor breast cancer immunotherapy, comprising:

(a) contacting a biological sample from a subject who is undergoing or has undergone breast cancer therapy with the composition of any embodiment or combination of embodiments of the disclosure; and

(b) determining an amount of antibodies against the one or more peptides in the bodily fluid sample;

wherein a decrease or no increase in the amount of antibodies relative to a control, such as a baseline level of antibodies in a similar bodily fluid sample from the subject indicates that the immunotherapy is ineffective in the subject.

The subject may be any suitable subject receiving breast cancer therapy, including but not limited to a human subject. As used herein, “breast cancer therapy” includes one or more of surgery to remove the primary breast tumor, radiation therapy, chemotherapy, and hormonal therapy.

A decrease in the amount of antibodies over time compared to a baseline level (i.e.: before breast cancer therapy initiation) indicates a favorable treatment response, while no decrease, or an increase, in antibody levels indicates a non-favorable treatment response. The methods can be carried out at any suitable time after breast cancer therapy begins as determined by attending medical personnel in light of all factors. In various non-limiting embodiments, the methods may be carried out at least 1 week, 2 weeks, 3 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 12 months, 18 months, 24 months, etc. after the beginning of therapy. As will be understood by those of skill in the art, the methods can be carried out any number of times for a given subject as deemed appropriate by attending medical personnel. Thus, the methods can be carried out 1, 2, 3, 4, 5, 6, 7 8, 9, 10, or more times for a given subject, to monitor the course of therapy. As will be understood by those of skill in the art, the methods can be carried out during the therapy, and can also be carried out after completion of the therapy, to monitor for possible breast cancer recurrence.

In all of the methods disclosed herein, the methods may include the use of additional antibody detection markers and controls as is appropriate for an intended use of the composition. The contacting can be carried out under any suitable conditions for promoting binding between the antibodies in the biological sample and the peptide array to form a binding complex that can be detected. Appropriate such conditions can be determined by those of skill in the art based on the intended assay, in light of the teachings herein. Similarly, any suitable additional steps can be used in the methods, such as one or more wash or other steps to remove unbound antibodies.

Any suitable detection technique can be used, including but not limited to enzyme linked immunosorbent assays (ELISA), bead based assay platforms such as the LUMINEX® systems, and 2-D array based assay platforms such as SEARCHLIGHT®. In one embodiment, the peptide arrays can be placed on a solid support, such as in a microarray, glass slide, membrane, microplate format or beads. The embodiment facilitates use of the compositions. Exemplary such assays are provided in the examples.

Similarly, any suitable biological sample can be used, including but not limited to a serum sample, plasma sample or blood sample from the subject. A “plasma sample” means blood plasma, the liquid component of blood, and is prepared, for example, by centrifugation of whole blood to remove blood cells. A serum sample is a plasma sample in which blood clotting factors have been removed.

In one embodiment, when no decrease is determined in the amount of antibodies relative to a baseline level of antibodies in a similar bodily fluid sample from the subject, the method may further comprise altering the breast cancer therapy being administered to the subject. Since the lack of antibody decrease indicates a non-favorable therapeutic outcome for the subject, this embodiment permits modifying the therapy as deemed appropriate by attending medical personnel (i.e.: increased dosage, change in treatment, etc.) to achieve a more favorable therapeutic outcome.

Examples

Recent advances in cancer immuno-therapeutics such as checkpoint inhibitors, chimeric antigen-receptor T cells, and tumor infiltrating T cells (TIL) are now significantly impacting cancer patients in a positive manner. Current reports indicate no more than 25% of cases result in complete remission. One of the limitations of these treatments is the identity of putative cancer antigens in each patient as it is technically challenging to identify of cancer antigens in a rapid fashion. Thus, identification of cancer antigens followed by targeted treatment will increase the efficacy of cancer immunotherapies.

We hypothesized that current immunomodulatory therapies are not highly effective for a large majority of cancer patients because 1) tumor antigens are not known, 2) strategies of boosting targeted anti-tumor response using tumor antigens is not a common treatment strategy, and 3) sufficient cooperation and stimulation between T, B, and dendritic cells are not promoted, and 4) a general strategy to relieve suppressive tumor microenvironment, such as checkpoint inhibition is not part of the standard therapies. To identify tumor-derived antigenic targets and to gain molecular insights into anticancer immunity, we have developed an integrative genomics-driven immunoproteomics platform (GDI). Using deep sequencing to identify mutations in the coding regions of 348 genes from 15 breast cancer patients, we designed personalized peptide microarrays. These microarrays contain mutant peptides and corresponding wild type counterparts. Incubating these personalized peptide microarrays with sera from respective patients revealed immunoreactive tumor antigens recognized by antibodies. In addition, we designed peptide microarrays based on high-frequency mutations extracted from two breast cancer studies and 9000 cancer genomes compiled in the COSMIC™ database, allowing us to identify high-frequency mutations that invoke immune response in cancer patients. Moreover, whole-genome sequencing and examination of personalized peptide microarrays of three breast cancer patients was carried out. Overall, we report the identification a total of 149 putative cancer antigens. We propose a strategy to eradicate cancer focusing on the GDI-based rapid identification of putative tumor antigens, monitoring the cancer patients' immune response, and utilization of tumor antigens in anticancer therapeutics.

Materials and Methods Patient Sample Selection and Characterization

The study to analyze de-identified tumor tissues and sera samples from breast cancer and benign cancer samples were approved by the UCHC Institutional Review Board (IRB). De-identified patients' discarded materials, 15 tumor samples and 15 benign samples, were collected by the UCHC Tissue Biorepository Core, tumor samples and adjacent normal tissues were subjected to next generation genomic sequencing, and tumor associated variants (SNVs, insertions, deletions) were determined using the Genesifter™ software tool. Matching sera from these patients were used to test the presence of mutation-specific antibodies in patients' sera by mutant-peptide microarrays. Briefly, in-depth targeted genomic DNA sequencing of 348 genes was carried out in cancer patients' tissue samples. Since benign cancers tissue samples were not readily available for next generation sequencing experiments, mutation analysis was carried out only in the malignant cancer samples. From the 15 malignant cancer samples sequenced for 348 genes, three malignant cancer patients were subjected to whole exome sequencing for 25,000 genes using cancer tissues and adjacent normal regions. Only the mutation detected specifically in the cancer tissues (after the comparative analysis with the adjacent normal tissues) from whole exome sequencing was then used to design the V5 peptide microarrays. Sera was collected from both malignant and benign cancer patients and tested for immunogenicity against mutant peptides using the V1-5 peptide microarrays. A minimum of two technical replicates were performed for each peptide microarray design.

Targeted Sequencing

A targeted SureSelectXT™ HiSeq sequencing study (Agilent Technologies, Danbury, Conn.) was designed to capture exome regions of 348 genes of interest in 15 breast cancer patients. The list of 348 genes was assembled from common breast cancer genes based on published reports; genes mutated in multiple breast cancer patient samples of recently published studies; genes with immunogenic mutant peptides, based on preliminary peptide chip results; genes with mutant spot intensities in the top 10%, based on preliminary chip results; additional recognized oncogenes; and interactors of transcription factors inducing pluripotent stem cells, retrieved from the Human Protein Reference Database. Custom baits for 348 genes were designed using SureDesign™, Agilent's online design tool. Approximately 3 ug of gDNA were extracted from each of 15 de-identified breast cancer patient tissue samples obtained from John Dempsey Hospital, University of Connecticut Health Center, with a NucleoSpin™ tissue kit (Macherey-Nagel). Library preparation and capture were then carried out by PerkinElmer with the extracted gDNA, using a SureSelectXT™ custom library and reagent kit purchased from Agilent Technologies.

The GRch37/hg19 Homo sapiens assembly was used in the design of the exome capture kit for the 348 genes. 68262 probes comprising a total of 2.7 Mbp provided bp coverage of 99.72%, with a probe tiling density of 4×. Target databases included RefSeq™, Ensembl™, CCDS™, Gencode™, VEGA™ and SNP™. The target region included coding exons of the 348 genes with an extension of 10 bps from the 3′ and 10 bps from the 5′ ends. Read length was 100 bps. Sequencing results were analyzed in the lab using PerkinElmer's online Genesifter™ tool. For each of the 15 breast cancer tissue samples, missense variants with an alternate read count >29 were selected for immunogenicity testing on personalized peptide chips.

Creating Peptide Arrays

In this study, four basic peptide chip designs (V1-V5) were developed and tested for differential binding affinity of mutant (mut) versus corresponding wild type (wt) peptides to antibodies in patient serum samples. Chip designs included personalized peptide arrays and three sets of diagnostic arrays. Fifteen personalized peptide chips (V1) contained duplicate sets of a variable number of wt-mut peptide pairs. Each personalized chip contained the unique set of filtered missense mutations identified in that patient's tumor sample in a SureSelectXT™ HiSeq sequencing study, paired with the wt counterparts, ranging from 460-746 wt-mut pairs among the 15 arrays. An additional set of commonly reported cancer mutations was added to each chip in a common, ‘diagnostic’ region at the bottom of the microarray.

In addition to the personalized arrays, three versions of diagnostic chips were designed. The initial diagnostic chip (V2) comprised triplicate sets of 1390 wt-mut peptide pairs. The second diagnostic chip (V3) contained a single set of 3071 wt-mut pairs, which merged the original unique wt-mut pairs from V2 with missense mutations from a more recent breast cancer study²⁰. For the third diagnostic chip (V4), highly mutated sites from the COSMIC™ database were retrieved to create an array of 593 singlet wt-mut pairs. Filtering criteria for the retrieved mutations were (1) site count (i.e., total mutations at a given site) >17 and (2) specific mutation count >=10. Each V4 chip contained five identical arrays of 593 wt-mut pairs each.

Incubation of Peptide Microarrays

Each peptide microarray was first rehydrated for 10 min with 1 ml of standard buffer (0.5% Tween 20 in PBS pH7.4) in room temperature. Overnight incubation with blocking buffer (1% BSA, 0.5% Tween 20 in PBS pH7.4) was carried out at 4 degrees in continuous shaking at 200 rpms. Peptide arrays were washed 3×1 min with standard buffer and incubated with the corresponding patient sera diluted in staining buffer (1:25 dilution in staining buffer—0.5% Tween 20, 0.1% BSA in PBS pH7.4). We had tested 1:10, 1:25, 1:50, and 1:500 dilutions using peptide microarrays. We found that although the lowest dilution (1:10) and the highest dilution (1:500) showed similar qualitative results, the best quantification for mutant:wild type ratios can be achieved at 1:25 serum dilution. Therefore, after careful analysis of the data from multiple dilutions, we have chosen to use 1:25 dilution as a way to assay for detection of breast cancer tumor antigens. Sera from each patients are diluted in staining buffer incubated with peptide microarrays for overnight at 4 degrees Celsius. Standard buffer was then used for 3 consecutive washes (3×10 min each) in room temperature after the overnight incubation. Next, peptide microarrays were incubated with goat anti-human IgG secondary antibody CY3-bound (1:1000 in staining buffer) for half an hour, followed by 3 more washes with standard buffer and a final wash with deionized water. The peptide microarrays were then dried, scanned using a GenePix™ 4000B scanner and analyzed using GenePix™ Pro 6.0 software, converting each spot into its mean and median pixel intensities.

Assessing Differential Mutant Binding Affinity

We first tested and validated the peptide microarray platform variability by generating peptide microarrays with increasing number of positive control peptides (1, 2, 3, 6, and 9 spots each), incubated the microarrays with patients' sera, and quantified the results to establish the spot-to-spot variation. Across multiple peptides, we found that the peptide microarrays are highly reproducible and standard deviations range between 5-20%.

Second, in order to achieve a robust statistical selection of immunogenic peptides, we utilize the power law global error model (PLGEM) statistics²⁶. Briefly, fluorescent intensities of wild type versus mutant peptide spots (for each duplicate set of wt-mut pairs) were compared using the PLGEM in order to identify statistically significant intensity differences. PLGEM software was downloaded from www.bioconductor.org and run in-house. A cutoff p-value of 0.01 was used as an initial filter for significance. Additionally, multiple chips were incubated with the same serum and only mutations showing the same immunogenic trend in two or more chips were retained in the significance list.

Immunoreactive mutant and wild type peptides were also assessed using the Kyte-Dolittle Algorithm to rule out physiochemical-based non-specific interactions with sera. We found that immunoreactivity is independent of the GRAVY scores, indicating the specificity of antibody interaction with peptide sequences. Multiple biological and technical replicates using peptide microarrays revealed consistent results. For the personalized peptide chips (V1), fluorescent intensities of wt versus mut peptide spots within each duplicate set of wt-mut pairs were compared using the power law global error model (PLGEM) in order to identify statistically significant intensity differences²⁶. For the first diagnostic chip (V2), a t-test was used to compare fluorescent intensities within each triplicate set of wt-mut pairs. A cutoff p-value of 0.05 was used as the initial filter. The second and third diagnostic chips (V3-V4) had no replicate spots. The whole exome chips (V5) were synthesized with duplicate spots for the wild type and mutant peptides. In this case, the initial test for significance was a check that there was no overlap between 99% confidence intervals (CI) around the mutant mean intensity and the wt mean intensity for each wt-mut pair of spots. CI was computed as the raw mean+/−z(0.01)*stdev/sqrt(576), where 576=number of pixels in computation of raw mean, stdev is the standard deviation of the mean of 576 pixel intensities, and z(0.01)=2.575²⁷.

For all microarrays, a second filter was then applied, retaining only those mutants whose mut/wt mean and median ratios were both greater than 2.0 (>1.5 for V4, V5). Requiring both mean and median ratios to pass the filter reduced the number of artifacts which remained in the significance list. Artifacts were caused mainly by intensity spillover from adjacent spots, or extraneous spots on the chip. Additionally, where multiple chips were incubated with the same serum, only mutations showing the same immunogenic trend in two or more chips were retained in the significance list. Once the initial filters were applied, a final visual inspection of the significant spots was required to remove any remaining entries whose intensity differences were due to artifacts. No statistical difference in the amount of reactive peptides per gene between the 348 gene array and whole exome array was observed.

Multiplex PCR Amplification and Next Generation Sequencing of IgH and IGKL CDR3 Sequences

To generate the template library for the Illumina HiSeq™ machine, a multiplex PCR system was designed to amplify rearranged IgH and IGKL loci from genomic DNA using methods previously described²⁸. Multiple consensus forward primers, each specific to a functional IgH V, IgL V, and IgK V segments are amplified using consensus reverse primers from J segments. The amplified products are used for the library construction and sequencing using the Illumina HiSeq System, which generates reads of length 110 bp and covers the entire range of CDR3 lengths, sequencing from the J to the V region. All sequencing was performed at Adaptive Biotechnologies Corp.

Preprocessing of Genome Analyzer Sequence Data

Raw HiSeg™ sequence data were preprocessed to remove errors in the primary sequence of each read and to compress the data. Among the three cancer tissue samples analyzed, approximately 10-13% of the sequences from IgH and 37-42% of the IgKL sequences from the HiSeq™ were technical failures and were removed by a complexity filter and a nearest neighbor algorithm was used to collapse the data into unique sequences as described²⁹. Data analysis was performed as previously described²⁸.

Results Development of Genomic-Driven Immunoproteomics Platform

We have collected and performed deep sequencing of high-frequency cancer genes. The variants identified from each patient served as a template to design a patient-specific peptide array. This personalized array then served as an identification platform for the discovery of antigenic targets, using serum from each corresponding patient.

Thus, genomic variants on coding exons of 348 frequently mutated cancer genes from 15 breast cancer patients' tumors were subjected to exome capture followed by deep sequencing, resulting in a mean read-depth of over 900 (Table 2). This deep sequencing strategy allowed the detection of mutations in regions of cancer tissue even when the distribution of cancer cells was extremely low. As a result, all 348 genes were successfully captured and sequenced, resulting in the identification of 460-746 unique missense variants from each patient, including variants in cancer driver genes such as BRCA1, BRCA2, TP53, MLL3, and NCOR1. Indeed, a substantial number of new variants were identified in breast cancer through the deep sequencing method. Although the exact function of the detected variants in cancer is not known, their identification permitted us to investigate their potential antigenicity in each patient.

TABLE 2 Summary of immunogenic variant peptides identified by V1 peptide microarrays: Personalized peptide microarrays were incubated with corresponding patients' sera, peptides were quantified, and the PLGEM statistical analysis was calculated (as described in the Materials and Method Section). Note that only limited numbers of putative tumor antigens were identified from over 2000 unique peptides tested. Immuno- reactivity (MT/WT Patient Cancer Genes Intensities) Codon Experiment Patient 1 MUC17 5.25 T959A NextGenSeq Patient 1 MUC17 4.63 T2786A NextGenSeq Patient 5 PCSK5 3.03 T1343M NextGenSeq Patient 1 NCOR1* 2.54 K178N NextGenSeq Patient 5 INF2L2 2.31 E79K NextGenSeq Patient 1 OBSCN 2.18 V1600D NextGenSeq Patient 3 IALPK 2.18 P1449S NextGenSeq Patient 2 MUC17 2.06 S1083P NextGenSeq Patient 4 TTN 2.02 K1155E NextGenSeq Patient 1 BRCA1* 1.98 E1038G NextGenSeq *Driver Cancer Genes

Discovery of Nine Genomically Verified Breast Putative Cancer Antigens Using Personalized Peptide Microarrays

In the next step, translation of the genomic sequencing data into a patient's personalized immunological assessment, termed GDI, was achieved through an innovative platform of personalized peptide microarrays, each one designed for a specific patient based on that patient's set of sequenced variants. These personalized peptide microarrays, comprising 460-746 duplicate pairs of 15-mer wild type (wt) and corresponding mutant (mut) peptides, were synthesized using amino acid particle-based technology, which allows the generation of thousands of unique peptides directly on a single glass slide. Patient-specific personalized peptide microarrays, termed V1 chips, were tested against matching patients' sera to identify the antigenic mutant peptides among those mutations, discovered through genomic sequencing. Antibodies present in serum from patient 1 reacted specifically to five mutant peptides, but not to their wt counterparts. Quantification of each of the five peptide spots on the personalized peptide array and statistical analysis indicated significant immunoreactivity to BRCA1 (E1038G), NCOR1 (K178N), OBSCN (V1600D), and MUCIN 17 (T2786A and T959A). Out of 2047 variants tested altogether among 15 breast cancer patients, we found nine genomically verified mutations that invoked a strong immune response (Table 2). These results indicate that immunogenic variants are relatively rare among the variant landscape of an individual cancer genome, so that a systematic method for their identification is crucial. Using the GDI platform, detection of immunogenic mutations, specific to each cancer patient, can be achieved rapidly.

Detailed analysis of peptide microarrays revealed that genomic variants shared among multiple patients failed to invoke a common antibody-mediated immune response in all the patients carrying these mutations. For example, the BRCA1 (E1038G) genomic mutation was found in five breast cancer patients; yet, the antibody-mediated immune response was invoked only in Patient 1. Similarly, NCOR1 (K178N) mutation was found in all 15 patients, but invoked an immune response in only one patient. Additional examples were observed for OBSCN, MUCIN17, IALPK, TTN, and PCSK5; in each of these cases of shared genomic variants, most patients failed to invoke an antibody-mediated immune response. These results highlight that a defective immune response against common mutant proteins predominates in most cancer patients.

Identification of 53 Putative Cancer Antigens Using Publically Available Cancer Databases

In order to identify additional genome-wide breast cancer associated mutations beyond the 348 genes examined, three diagnostic peptide microarrays were designed and tested. Two diagnostic microarrays, namely V2 and V3 chips, were designed based on mutations that have been identified by two large scale genomic sequencing studies in breast cancer. The third diagnostic microarray (V4) was designed utilizing high-frequency mutations extracted from over 9000 cancer genomes curated in the Cosmic database. Testing the diagnostic peptide microarrays with sera from 15 breast cancer patients and 15 benign cancer patients resulted in the identification of 53 additional genomic mutations that invoked an immune response. Thus, combining positive data from V1-V4 microarrays resulted in the identification of 62 putative cancer antigens, among which 53 are high-frequency mutation sites.

Whole Genome GDI Analysis of Three Cancer Patients Resulted in Identification of 35-50 Immunogenic Putative Cancer Antigens Per Patient

Since 348 genes represent a small fraction of ˜25,000 genes of the human genome, we tested the presence of tumor antigens at a whole protein-coding genome/exome level. Thus, we sequenced the whole exomes of three breast cancer tissues and adjacent normal regions, identified mutations that are exclusively present in the tumor tissues, and designed personalized peptide microarrays populated with mutant and corresponding wild type peptides based on the genomic sequencing. We found that wild type and mutant peptides derived from genomic sequencing of normal and cancer regions of patient 1 (585 mutations) and patient 2 (576 mutations) resulted in peptides that can fit into one slide. However, genomic DNA sequencing of patient 6 resulted in the identification of 3775 mutations, resulting in the populating these mutations on two microarrays. In addition, we also populated the peptide microarrays with high frequency mutations from the COSMIC′ database. Subsequent testing of these peptide microarrays using sera from respective patients were carried out. When compared to the sequencing of 348 genes, whole exome sequencing resulted in increased number of genomic mutations that showed strong reaction to cancer-associated mutations. In total, 35-50 immunogenic mutant peptides were identified in each patient, among which substantial increase in the total number of putative tumor antigens/antigenic peptides that are verified by whole genomic sequencing (Table 1). Detailed analysis of these whole exome microarrays revealed immune response against mutant peptides derived from the patient as well as from the COSMIC database (Table 1). In total, combining data from V1-V5 arrays, we identified 149 immunogenic peptides that invoke immune response in cancer patients, among which 20 are insertions, 59 are deletions, and 70 are SNVs (Table 1). These results reveal that there is a wide-spread antibody response targeting mutant amino acids including the single-nucleotide variants.

DISCUSSION

This study identified genomic mutations on the protein coding exons of breast cancer patients and detected immune reactivity against subset of these mutations using peptide microarrays. The first sequencing study, focused on 348 commonly mutated cancer associated genes in 15 breast cancer patients, revealed that only a small subset (nine) of mutated genes are immunologically reactive to antibodies present in patient sera. Expanding the number of investigated genes to the whole exome-level and testing for antibody response revealed much higher number of putative cancer antigens in all three patients examined; 35 genomically verified mutations were found to have strong immune response. These results suggest that although there are hundreds to thousands of mutations in the protein coding regions of cancer genomes, only a minor subset of mutant proteins can invoke antibody-mediated immune response. This phenomenon may be due to multiple influencing factors such as the abundance of mutant proteins in cancer cells, the affinity of mutant peptides to the expressed HLA receptors, presence of efficient antigen presentation and lymphoid circulation, and overcoming the immune suppressive tumor microenvironment. Interestingly, when high-frequency cancer-associated mutations from COSMIC′ database and from two other breast cancer studies were examined, additional putative breast cancer antigens were discovered (Table 1). Overall, these results support the hypothesis that widespread genomic mutations in protein coding exons of human breast cancer patients can invoke an immune response targeted against the mutant peptides. Specifically this investigation has led to the identification of 149 cancer-specific immunogenic antigens, providing strong evidence that mutant proteins can be recognized by the immune system, and these invoke an antibody-mediated immune response (Table 1). Interestingly, this investigation resulted in the identification of a number of new cancer associated mutations not previously reported in the COSMIC™ database or other studies. One possible explanation for this observation is due high read-depth of genomic sequencing, which allows sensitive detection of mutations. This finding was also confirmed by sequencing germline DNA from normal tissues of three patients and compared the data with sequence data from matching tumor DNA. It is only beginning to be recognized by leading cancer researchers that there is a so called “dark matter” in the cancer genome, referring to the gene mutations that are commonly missed because of low sequencing depth typically used. Consistent with this notion, when ultra-deep sequencing was performed on normal eyelids of five individuals sequencing at 500 read-depth/gene on 74 genes, a number of new mutations on oncogenes were discovered.

This investigation also introduces a discovery platform, termed the GDI, that allows rapid translation of mutational profiles generated from genomic sequencing of cancer patients into an immunological test, which can be used to assess patients' immunological profile as well as discovering putative antigenic targets. Further, this platform is useful for monitoring the immunological response of different types of existing immunotherapies/checkpoint inhibition such as anti-CTLA-4, anti-PDL-1, and anti-PD-1. Currently, patients undergoing these immunotherapies are monitored for tumor shrinkage, approximately several weeks after treatment by computed tomography (CT) or magnetic resonance imaging (MRI). While imaging modalities are useful to determine the response rate, immunological status and the correct dosage cannot be assessed accurately and fine-tuned for optimal response. Using the GDI methodology can potentially provide direct assessment of cancer patients' immune status. For example, patients who do not show detectable antibody response against cancer-associated mutant proteins before or after checkpoint inhibition therapies are likely to be poor candidates for continued treatment with these agents. On the other hand, patients who show no immune response against mutant proteins before the treatment but mount a strong response after checkpoint inhibition therapies may be good candidates for continued treatment. Further, immunological readouts for patient-specific cancer mutations can be measured before, during and after immunotherapy using this platform using a simple blood test, so that optimal tumor killing can be correlated with the quantifiable signals measured by GDI-based personalized peptide arrays. Finally, tracking T-cell mediated immune response against the patient-specific mutants throughout treatment of checkpoint inhibition is quite challenging. Since antibody-mediated B cell response requires T-helper cells recognizing the tumor antigen and stimulating specific B cell clones, quantification of antibody response may assist in determining the proper checkpoint inhibitor dosage in a patient specific manner.

Since the GDI platform measures antibody-mediated immune response directly against mutant proteins (which also requires T_(H) cell-mediated B cell activation), the use of GDI-based peptide microarray as a companion diagnostic blood test will provide additional quantifiable measurements, such as the number and extent of antibody binding to mutant proteins. Frequent monitoring of cancer patients before, during, and after the checkpoint inhibition using the GDI platform will allow standardization of immunotherapies by assessing quantifiable measurements of patients' immune reaction against tumor-specific mutant proteins. The GDI platform is also useful for the checkpoint inhibitor drug dosing of individual cancer patients at the immunological level, and may allow more accurate categorization of true responsive versus non-responsive patients.

The personalized peptide microarrays that we have utilized for the first time have application for immunotherapy, such as selecting vaccine epitopes for cancer patients. Previous efforts to treat cancer using peptide vaccines have not been widely efficacious, possibly because there is not a straightforward assay to select strong antigenic epitopes relevant to each patient. Utilizing antigenic peptides based on the GDI method is an efficient way to select relevant vaccine targets. In patients that respond to mutations immunologically, boosting the immune system with a peptide vaccine containing antigenic targets may help eliminate the tumor directly. Further, peptide microarrays can be used to monitor the immune response during vaccine-based immunotherapy in cancer patients.

Examination of tissue sections of all patients revealed that there is a strong correlation between presence of immune cell infiltration in the cancer tissues and antibody response seen at the peptide microarray level.

Based on our study design, we were able to identify and evaluate two interesting categories of antibody response—one being the response against mutant proteins that are found in the genomic DNA of tumor tissues (from V1 and V5 personalized chips), and the other being the response against mutant proteins not detected in the genomic DNA of tumor tissues examined (from V2-4 diagnostic chips). For example, although four variants of TP53 (P72R, R248Q, D281H, Y234N) were identified in the deep sequencing of 15 breast cancer tissue samples, none of these genomic mutants of TP53 was found to invoke an immune response in the breast cancer patients examined. However, when additional site-specific and frame-shift mutations of TP53 and CDKN2A reported in the COSMIC database were tested in diagnostic peptide microarrays, immune response against nine TP53 site-specific mutations and nine frame-shift mutations, as well as four CDKN2A frame-shift mutations were detected in patient serum, even though these mutations were not detected in the DNA from breast cancer tissues that were sequenced in this study (Table 1). The reason for detecting antibody responses in cancer patients against mutant proteins not verifiable at the exomic DNA level is unclear at present. One likely explanation is that while DNA is not mutated, multiple RNAs are mutated due to errors in RNA editing mechanisms. Also, RNA translational errors may result in mutated proteins. Indeed, an integrative study on human disease tissues at the DNA, RNA, protein, and immunological levels revealed similar phenomenon⁴⁴. Similar findings have also been reported in a number of large-scale cancer omics studies, in which differences in DNA and RNA mutations have been documented⁴⁵.

Another possible explanation is that mutations arising from other organs and tissues over the life span of patients, which invoked systemic antibody response against these mutant proteins produced from memory B cells, may linger in patients' bloodstream. In this scenario, genomic sequencing of cancer tissues will not capture the entire mutation repertoire in many other tissues and will be discordant with antibody responses. Indeed, sequencing of normal eyelids from five subjects revealed many oncogenic mutations including TP53 and CDKN2A genes, indicating that widespread DNA mutations is a common occurrence³⁴. Further, due to the well know phenomena of clonal drifting of cancer cells, immune system may only eliminate a subset of cancer clones. In this scenario, antibody response may continue to be present in the patient's sera, as detected by peptide microarrays, while the genomic mutation signature may have been eradicated by the immune system.

It is interesting that when we first examined immune response against mutant proteins from 348 genes, we found that very few mutant peptides invoked immune response in breast cancer patients. However, when we analyze the whole exomes of three patients and tested all the mutations on microarrays, we found substantially more immune reactive mutant peptides. Corresponding wild type peptides did not show detectable level of immune reactivity. These results suggest that immune response against mutant peptide is specific and unlikely to be due to nonspecific autoantibody binding.

In summary, our results indicate that antigenic targets of frequently mutated cancer genes can be screened in a high-throughput manner by the GDI platform described in this paper. The combination of deep genomic sequencing and personalized peptide arrays based on sequencing results offers a novel platform for uncovering new cancer-specific antigenic targets and may help identify effective anti-cancer treatment regimens. The high-throughput assay of GDI-based peptide microarrays has the distinct advantage of streamlined antigenic peptide identification and may offer a seamless translation from genomics sequencing data into actionable blood test that can quantify and monitor immune response of patients.

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1-14. (canceled)
 15. A method for identifying antigenic targets for breast cancer treatment, comprising: (a) contacting a peptide array with a biological sample from a subject having breast cancer, wherein the peptide array comprises at least 25 mutant peptides selected from the group consisting of SEQ ID NOS: 1-82, 84-91, and 93-149, or polypeptides comprising the mutant peptides; wherein the array comprises mutant peptides encoded by 10 or more genes, and wherein the mutant peptides are fluorescently labeled; (b) detecting binding of antibodies in the serum to the mutant peptides and the wild-type counterparts thereof, thus identifying antigenic targets for therapy in treating the subject.
 16. A method for monitoring breast cancer immunotherapy, comprising (a) contacting a biological sample from a subject who is undergoing or has undergone breast cancer immunotherapy with an isolated composition, comprising at least 25 mutant peptides selected from the group consisting of SEQ ID NOS: 1-82, 84-91, and 93-149, or polypeptides comprising the mutant peptides; wherein the composition comprises mutant peptides encoded by 10 or more genes; and (b) determining an amount of antibodies against the mutant peptides in the bodily fluid sample; wherein an increase in the amount of antibodies relative to a control, such as a baseline level of antibodies in a similar bodily fluid sample from the subject indicates efficacy of the breast cancer immunotherapy in the subject; and wherein a decrease or no increase in the amount of antibodies relative to a control, such as a baseline level of antibodies in a similar bodily fluid sample from the subject indicates that the immunotherapy is ineffective in the subject.
 17. The method of claim 15, wherein the peptide array further comprises 25 or more wild type peptide counterparts to the mutant peptides, or polypeptides comprising the wild type peptides.
 18. The method of claim 17, wherein the total number of mutant and wild type peptides, or polypeptides comprising the mutant and wild type peptides, is 100,000 or less.
 19. The method of claim 17, wherein the total number of mutant and wild type peptides, or polypeptides comprising the mutant and wild type peptides, is 1000 or less.
 20. The method of claim 15, wherein the mutant peptides are immobilized on the surface of a solid support.
 21. The method of claim 16, wherein the composition comprises one or more wild type peptides corresponding to the mutant peptides, or polypeptides comprising the wild type peptides.
 22. The method of claim 16, wherein the composition comprises 25 or more wild type peptide counterparts to the mutant peptides, or polypeptides comprising the wild type peptides.
 23. The method of claim 22, wherein the total number of mutant and wild type peptides, or polypeptides comprising the mutant and wild type peptides, is 100,000 or less.
 24. The method of claim 22, wherein the total number of mutant and wild type peptides, or polypeptides comprising the mutant and wild type peptides, is 1000 or less.
 25. The method of claim 15, further comprising administered immunotherapy against the antigenic targets identified according to the method of claim
 15. 